3U21 | pdb_00003u21

Crystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein (residues 370-495) (NFRKB) from Homo sapiens at 2.18 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3U21/pdb

• Classification: Transcription regulation, DNA BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-30 Released: 2011-11-02 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.270 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Structure of a Novel Winged-Helix Like Domain from Human NFRKB Protein.

Kumar, A., Mocklinghoff, S., Yumoto, F., Jaroszewski, L., Farr, C.L., Grzechnik, A., Nguyen, P., Weichenberger, C.X., Chiu, H.J., Klock, H.E., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A., Conklin, B.R., Fletterick, R.J., Wilson, I.A.

(2012) PLoS One 7: e43761-e43761

• PubMed: 22984442 
• DOI: https://doi.org/10.1371/journal.pone.0043761
• Primary Citation Related Structures: 
  3U21


• PubMed Abstract: 
  

  The human nuclear factor related to kappa-B-binding protein (NFRKB) is a 1299-residue protein that is a component of the metazoan INO80 complex involved in chromatin remodeling, transcription regulation, DNA replication and DNA repair. Although full length NFRKB is predicted to be around 65% disordered, comparative sequence analysis identified several potentially structured sections in the N-terminal region of the protein. These regions were targeted for crystallographic studies, and the structure of one of these regions spanning residues 370-495 was determined using the JCSG high-throughput structure determination pipeline. The structure reveals a novel, mostly helical domain reminiscent of the winged-helix fold typically involved in DNA binding. However, further analysis shows that this domain does not bind DNA, suggesting it may belong to a small group of winged-helix domains involved in protein-protein interactions.

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Organizational Affiliation: 
• Joint Center for Structural Genomics, La Jolla, California, United States of America.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.03 kDa 
• Atom Count: 1,763 
• Modeled Residue Count: 217 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear factor related to kappa-B-binding protein	A, B	127	Homo sapiens	Mutation(s): 0  Gene Names: BC063280, INO80G, NFRKB
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P4R8 (Homo sapiens) Explore Q6P4R8  Go to UniProtKB:  Q6P4R8
PHAROS:  Q6P4R8 GTEx:  ENSG00000170322

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.270 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33U21

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.942	α = 90
b = 60.942	β = 90
c = 130.839	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2012-10-10
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.4: 2025-10-22
  Changes: Data collection, Refinement description, Structure summary